All ecosystems contain both sources and sinks for atmospheric carbon (C). A change in their balance of net and gross ecosystem carbon uptake, ecosystem-scale carbon use efficiency (CUE_ECO), is a change in their ability to buffer climate change. However, anthropogenic nitrogen (N) deposition is increasing N availability, potentially shifting terrestrial ecosystem stoichiometry towards phosphorus (P) limitation. Depending on how gross primary production (GPP, plants alone) and ecosystem respiration (R_ECO, plants and heterotrophs) are limited by N, P or associated changes in other biogeochemical cycles, CUE_ECO may change. Seasonally, CUE_ECO also varies as the multiple processes that control GPP and respiration and their limitations shift in time. We worked in a Mediterranean tree-grass ecosystem (locally called ‘dehesa’) characterized by mild, wet winters and summer droughts. We examined CUE_ECO from eddy covariance fluxes over 6 years under control, +N and + NP fertilized treatments on three timescales: annual, seasonal (determined by vegetation phenological phases) and 14-day aggregations. Finer aggregation allowed consideration of responses to specific patterns in vegetation activity and meteorological conditions. We predicted that CUE_ECO should be increased by wetter conditions, and successively by N and NP fertilization. Milder and wetter years with proportionally longer growing seasons increased CUE_ECO, as did N fertilization, regardless of whether P was added. Using a generalized additive model, whole ecosystem phenological status and water deficit indicators, which both varied with treatment, were the main determinants of 14-day differences in CUE_ECO. The direction of water effects depended on the timescale considered and occurred alongside treatment-dependent water depletion. Overall, future regional trends of longer dry summers may push these systems towards lower CUE_ECO.